Commit 78823aea authored by Sylvain Jasson's avatar Sylvain Jasson
Browse files

typos + added logos

parent 71bed1c0
......@@ -7,7 +7,7 @@ EXAMPLE_DIR = $(SRCDIR)/examples/three_parents_F2
all: user_manual.pdf
user_manual.pdf: spell-pedigree.tex detection.tex outputs.tex pipeline.tex pop.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg images/full_map.png .inputs .outputs
user_manual.pdf: spell-pedigree.tex detection.tex outputs.tex pipeline.tex pop.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg images/full_map.png images/logo_MIAT.png pdfs/by-sa.pdf pdfs/gpl-v3-logo.pdf .inputs .outputs
pdflatex --shell-escape user_manual.tex && pdflatex --shell-escape user_manual.tex
version.tex:
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......@@ -106,26 +106,27 @@ Note that you must use \texttt{output-nppop} processing option in \texttt{spell-
\subsection{full map}
The special text file named \texttt{full\_map.txt} is produced at the root of \texttt{my name.report} directory. The full genetic map is drawn using text characters. Any detected QTL is inserted in this map with its confidence interval (figure \label{fig:full-map}).
The special text file named \texttt{full\_map.txt} is produced at the root of \texttt{my name.report} directory. The full genetic map is drawn using text characters. Any detected QTL (for any trait under study) is inserted in this map with its confidence interval (figure \vref{fig:full-map}).
\begin{figure}[h]
\includegraphics[width=1.0\textwidth]{full_map.png}
\caption{screen capture of \texttt{full\_map.txt} in a terminal. The chromosome and markers are white. The found QTL and its confidence interval are displayed in green.}
\caption{screen capture of \texttt{less -RS full\_map.txt} in a \textit{ad hoc} resized terminal. Chromosome names are printed light blue. The chromosome and markers are white. The found QTL and its confidence interval are added in green labeled with trait name (\texttt{t1}), \texttt{@}, QTL position (\texttt{135.34}) and confidence interval (\texttt{[129.246:140.84]})}
\label{fig:full-map}
\end{figure}
Note that you must uses \texttt{cat} ou \texttt{less -RS} command in ordrer to see it properly, \texttt{less} ou your favorite text editor may fail to read special characters.
Note that you must use \texttt{cat} or \texttt{less -RS} command in ordrer to see it properly. \texttt{more} command, \texttt{less} command or your favorite text editor may fail to read special characters.
\subsection{Trait by trait reports}
For every trait on analysis, a report directory is generated (this directory name is the trait name). Whithin this directoty the report file itself is named after the trait name followed by \texttt{\_report.txt}
For every trait under analysis, a report directory is generated (this directory name is the trait name). Whithin this directoty the report file itself is named after the trait name followed by \texttt{\_report.txt}
This file is divided in several parts. For the sample file \vref{sample:report} they are :
\begin{description}
\item[General information (lines 1-7)] Trait name and what was detected (QTLs positions and confidence intervals)
\item[R2 (lines 12-20)] Part of the variance explained by each QTL
\item[Coefficients (lines 22-54)] Cross and QTLs allele effects are displayed with their estimated vairiance-covariance matrix
\item[Contrasts (lines 57-79 and 81-103)] Any tractable contrast is displayed and its significance tested. \texttt{spell-qtl} displays a contrasts section for every comparable effects group.
\item[Final Model (lines 105-351)] The final linear model for this detection is then displayed in human readable form. (It is available in computer form in files \texttt{trait\_values.txt} and \texttt{Model\_*X.txt})
\item[Coefficients (lines 22-54)] Cross effects and QTLs allele effects are displayed with their estimated vairiance-covariance matrix
\item[Contrasts (lines 57-79 and 81-103)] Any tractable contrast is computed and its significance tested. \texttt{spell-qtl} displays a contrasts section for every comparable effects group.
\item[Final Model (lines 105-325)] The final linear model for this detection is then displayed in human readable form. (It is available in computer readable form in files \texttt{trait\_values.txt} and \texttt{Model\_*X.txt})
\item[Final Model inversion (lines 328-351)] $(X^tX)^{-1}$ matrix from linear model solving in human readable form. (It is available in computer readable form in file \texttt{Model\_*\_XtX\_inv.txt}).
\end{description}
\lstinputlisting[numbers=left,
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......@@ -57,6 +57,16 @@ basicstyle=\ttfamily
\date{Version
\input{version.tex}
}
\publishers{\includegraphics[width=0.3\textwidth]{images/logo_MIAT.png}}
%\lowertitleback{This manual is licensed under a \href{https://creativecommons.org/licenses/by-sa/4.0/}{Creative Commons Attribution-ShareAlike 4.0 International License}.
%\begin{center}
%\includegraphics{images/by-sa.pdf}
%\end{center}}
\begin{document}
\maketitle
......@@ -66,9 +76,17 @@ basicstyle=\ttfamily
Spell-QTL\footnote{ {\em Species perscrutandis enixe locis locabutur} means {\em The characters will be localized using an zealous loci inspection}, the very purpose of the software}
is a software suite allowing to detect QTLs in any crossing design.
It is developed at MIAT lab by Damien Leroux and Sylvain Jasson. It is available (including the present user manual) at \url{https://mulcyber.toulouse.inra.fr/frs/?group_id=204} under Gnu Public License.
It is developed at MIAT lab by Damien Leroux and Sylvain Jasson. It is available at \url{https://mulcyber.toulouse.inra.fr/frs/?group_id=204} under Gnu Public License.
\vspace*{\fill}
\noindent Spell-QTL is available at \url{https://mulcyber.toulouse.inra.fr/frs/?group_id=204} under Gnu Public License.
\begin{center}
\includegraphics[clip, trim=0.5cm 8cm 0.5cm 14cm,width=0.25\columnwidth]{pdfs/gpl-v3-logo}
\end{center}
This manual is licensed under a \href{https://creativecommons.org/licenses/by-sa/4.0/}{Creative Commons Attribution-ShareAlike 4.0 International License}.
\begin{center}
\includegraphics[width=0.25\columnwidth]{pdfs/by-sa}
\end{center}
\input{pipeline.tex}
......
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